A bigger mouse? The rat genome unveiled

Molecular complexity of the major urinary protein system of the Norway rat, Rattus norvegicus

Major urinary proteins (MUP) are the major component of the urinary protein fraction in house mice (Mus spp.) and rats (Rattus spp.). The structure, polymorphism and functions of these lipocalins have been well described in the western European house mouse (Mus musculus domesticus), clarifying their role in semiochemical communication. The complexity of these roles in the mouse raises the question of similar functions in other rodents, including the Norway rat, Rattus norvegicus. Norway rats express MUPs in urine but information about specific MUP isoform sequences and functions is limited. In this study, we present a detailed molecular characterization of the MUP proteoforms expressed in the urine of two laboratory strains, Wistar Han and Brown Norway, and wild caught animals, using a combination of manual gene annotation, intact protein mass spectrometry and bottom-up mass spectrometry-based proteomic approaches. Cluster analysis shows the existence of only 10 predicted mup genes. Further, detailed sequencing of the urinary MUP isoforms reveals a less complex pattern of primary sequence polymorphism in the rat than the mouse. However, unlike the mouse, rat MUPs exhibit added complexity in the form of post-translational modifications, including the phosphorylation of Ser4 in some isoforms, and exoproteolytic trimming of specific isoforms. Our results raise the possibility that urinary MUPs may have different roles in rat chemical communication than those they play in the house mouse. Shotgun proteomics data are available via ProteomExchange with identifier PXD013986.

Rat mir-155 generated from the lncRNA Bic is 'hidden' in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters

MicroRNAs (miRNAs) are a class of small noncoding RNAs acting as post-transcriptional gene expression regulators in many physiological and pathological conditions. During the last few years, many novel mammalian miRNAs have been predicted experimentally with bioinformatics approaches and validated by next-generation sequencing. Although these strategies have prompted the discovery of several miRNAs, the total number of these genes still seems larger. Here, by exploiting the species conservation of human, mouse, and rat hairpin miRNAs, we discovered a novel rat microRNA, mir-155. We found that mature miR-155 is overexpressed in rat spleen myeloid cells treated with LPS, similarly to humans and mice. Rat mir-155 is annotated only on the alternate genome, suggesting the presence of other "hidden" miRNAs on this assembly. Therefore, we comprehensively extended the homology search also to mice and humans, finally validating 34 novel mammalian miRNAs (two in humans, five in mice, and up to 27 in rats). Surprisingly, 15 of these novel miRNAs (one for mice and 14 for rats) were found only on the alternate and not on the reference genomic assembly. To date, our findings indicate that the choice of genomic assembly, when mapping small RNA reads, is an important option that should be carefully considered, at least for these animal models. Finally, the discovery of these novel mammalian miRNA genes may contribute to a better understanding of already acquired experimental data, thereby paving the way to still unexplored investigations and to unraveling the function of miRNAs in disease models.

Localization of pre- and postsynaptic cholinergic markers in rodent forebrain: a brief history and comparison of rat and mouse

Rat and mouse models are widely used for studies in cognition and pathophysiology, among others. Here, we sought to determine to what extent these two model species differ for cholinergic and cholinoceptive features. For this purpose, we focused on cholinergic innervation patterns based on choline acetyltransferase (ChAT) immunostaining, and the expression of muscarinic acetylcholine receptors (mAChRs) detected immunocytochemically. In this brief review we first place cholinergic and cholinoceptive markers in a historic perspective, and then provide an overview of recent publications on cholinergic studies and techniques to provide a literature survey of current research. Next, we compare mouse (C57Bl/J6) and rat (Wistar) cholinergic and cholinoceptive systems simultaneously stained, respectively, for ChAT (analyzed qualitatively) and mAChRs (analyzed qualitatively and quantitatively). In general, the topographic cholinergic innervation patterns of both rodent species are highly comparable, with only considerable (but region specific) differences in number of detectable cholinergic interneurons, which are more numerous in rat. In contrast, immunolabeling for mAChRs, detected by the monoclonal antibody M35, differs markedly in the forebrain between the two species. In mouse brain, basal levels of activated and/or internalized mAChRs (as a consequence of cholinergic neurotransmission) are significantly higher. This suggests a higher cholinergic tone in mouse than rat, and hence the animal model of choice may have consequences for cholinergic drug testing experiments.

Combining QTL data for HDL cholesterol levels from two different species leads to smaller confidence intervals

Quantitative trait locus (QTL) analysis detects regions of a genome that are linked to a complex trait. Once a QTL is detected, the region is narrowed by positional cloning in the hope of determining the underlying candidate gene-methods used include creating congenic strains, comparative genomics and gene expression analysis. Combined cross analysis may also be used for species such as the mouse, if the QTL is detected in multiple crosses. This process involves the recoding of QTL data on a per-chromosome basis, with the genotype recoded on the basis of high- and low-allele status. The data are then combined and analyzed; a successful analysis results in a narrowed and more significant QTL. Using parallel methods, we show that it is possible to narrow a QTL by combining data from two different species, the rat and the mouse. We combined standardized high-density lipoprotein phenotype values and genotype data for the rat and mouse using information from one rat cross and two mouse crosses. We successfully combined data within homologous regions from rat Chr 6 onto mouse Chr 12, and from rat Chr 10 onto mouse Chr 11. The combinations and analyses resulted in QTL with smaller confidence intervals and increased logarithm of the odds ratio scores. The numbers of candidate genes encompassed by the QTL on mouse Chr 11 and 12 were reduced from 1343 to 761 genes and from 613 to 304 genes, respectively. This is the first time that QTL data from different species were successfully combined; this method promises to be a useful tool for narrowing QTL intervals.

ABT-510 is an effective chemopreventive agent in the mouse 4-nitroquinoline 1-oxide model of oral carcinogenesis

Despite numerous advances, the 5-year survival rate for head and neck squamous cell cancer (HNSCC) has remained largely unchanged. This poor outcome is due to several variables, including the development of multiple primary tumors. Therefore, it is essential to supplement early detection with preventive strategies. Using the 4-nitroquinoline 1-oxide (4-NQO) mouse model, we sought to define an appropriate dose and duration of administration that would predict the histologic timeline of HNSCC progression. Additionally, we sought to determine the timing of the onset of the angiogenic phenotype. Finally, using ABT-510 as a proof-of-principle drug, we tested the hypothesis that inhibitors of angiogenesis can slow/delay the development of HNSCC. We determined that 8 weeks of 100 microg/mL 4-NQO in the drinking water was the optimal dosage and duration to cause a sufficient incidence of hyperkeratoses, dysplasias, and HNSCC over a period of 32 weeks with minimal morbidity and mortality. Increased microvessel density and vascular endothelial growth factor expression in hyperkeratotic lesions provided evidence that the initiation of the angiogenic phenotype occurred before the development of dysplasia. Importantly, ABT-510 significantly decreased the overall incidence of HNSCC from 37.3% to 20.3% (P = 0.021) as well as the combined incidence of dysplasia and HNSCC from 82.7% to 50.6% (P < 0.001). These findings suggest that our refinement of the 4-NQO model allows for the investigation of the histologic, molecular, and biological alterations that occur during the premalignant phase of HNSCC. In addition, these data support the hypothesis that inhibitors of angiogenesis may be promising chemopreventive agents.

Rats in the genomic era

The rat genome project and the resources that it has generated are transforming the translation of rat biology to human medicine. The rat genome was sequenced to a high quality “draft,” the structure and location of the genes were predicted, and a global assessment was published (Gibbs RA et al., Nature 428: 493–521, 2004). Since that time, researchers have made use of the genome sequence and annotations and related resources. We take this opportunity to review the currently available rat genome resources and to discuss the progress and future plans for the rat genome.

A zinc-finger like metal binding site in the nucleosome

UV spectroscopy demonstrated that chicken mononucleosomes bind Co(II) and Zn(II) ions at submicromolar concentrations in a tetrahedral mode, at a conserved zinc finger-like site, composed of Cys110 and His113 residues of both H3 molecules. Neither of these metal ions substituted for another, indicating a limited binding reversibility. Molecular modeling indicated that the tetrahedral site is formed by unhindered rotations around Calpha-Cbeta bonds in the side chains of the zinc binding residues. The resulting local rearrangement of the protein structure shields the bound metal ion from the solvent, explaining the observed lack of reversibility of the binding. Consequences of these findings for zinc homeostasis, metal toxicology and nucleosomal regulation are discussed.

From genes to aggressive behavior: the role of serotonergic system

Recent investigations in neurogenomics have opened up new lines of research into a crucial genetic problem-the pathway from genes to behavior. This paper concentrates on the involvement of protein elements in the brain neurotransmitter serotonin (5-HT) system in the genetic control of aggressive behavior. Specifically, it describes: (1) the effect of the knockout of MAO A, the principal enzyme in 5-HT degradation, (2) the association of intermale aggression with the polymorphism in the Tph2 gene encoding the key enzyme in 5-HT synthesis in the brain, tryptophan hydroxylase (TPH), and (3) the effect of selective breeding for nonaggressive behavior on 5-HT metabolism, TPH activity and 5-HT(1A) receptors in the brain. The review provides converging lines of evidence that: (1) brain 5-HT contributes to a critical mechanism underlying genetically defined individual differences in aggressiveness, and (2) genes encoding pivotal enzymes in 5-HT metabolism (TPH and MAO A), 5-HT-transporter, 5-HT(1A) and 5-HT(1B) receptors belong to a group of genes that modulate aggressive behavior.